----------------------- Need shift 5 command (have more than 9 arguments): ----------------------- ----------------------- Start of variable list: ----------------------- SCRIPT_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_15_lncRNA_featureCounts Dataset_DIR: /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana Dataset_Label: GSE118757 ANNOTATION_FILE_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files ANNOTATION_FILE: /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt CONDITION_1_NAME: Ezh12M_P14 CONDITION_2_NAME: Ezh12F_P14 Lengths_DIR: /unprotected/projects/waxmanlab/routines/GTF_Files/lengths GENE_LENGTHS_FILE: intronic_only_gene_models_ncRNA_for_counting_lengths.txt COUNT_DIR: LncRNA_Intronic_Only_GTF OUTPUT_PREFIX: DiffExp_v2_LncRNA_Intronic_Only DiffExp_Index: DiffExp_15g COL_SUFFIX: LncRNA_Intronic_Only COUNT_PROGRAM: featureCounts ----------------------- End of variable list ----------------------- ========================================================== Starting on : Tue Mar 17 10:27:34 EDT 2020 Running on node : scc-kb7 Current directory : /net/waxman-server/mnt/data/waxmanlabvm_home/kkarri/Dana/Scripts/08c_DiffExp_15_lncRNA_featureCounts Current job ID : 3911212 Current job name : Step_08c_DiffExp_15g Task index number : undefined Parameter for multiple cores : 1 ========================================================== Change dir to scratch directory Print scratch directory location: /scratch/3911212.1.linga Loading required modules... ------------------------------------------ Sample_DIR: Ezh12M_1 Sample_ID: Ezh12M_1 Description: Ezh12M_1 M_Num: 1 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder Sample_DIR: Ezh12M_2 Sample_ID: Ezh12M_2 Description: Ezh12M_2 M_Num: 2 Copy Condition_1 sample count files to Condition_1 folder Copy Condition_1 sample count summary files to Condition_1 folder M_Num_Cond1_List: 12 ------------------------------------------ ------------------------------------------ Sample_DIR: Ezh12F_1 Sample_ID: Ezh12F_1 Description: Ezh12F_1 M_Num: 1 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_2 Sample_ID: Ezh12F_2 Description: Ezh12F_2 M_Num: 2 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_3 Sample_ID: Ezh12F_3 Description: Ezh12F_3 M_Num: 3 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_4 Sample_ID: Ezh12F_4 Description: Ezh12F_4 M_Num: 4 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder Sample_DIR: Ezh12F_5 Sample_ID: Ezh12F_5 Description: Ezh12F_5 M_Num: 5 Copy Condition_2 sample count files to Condition_2 folder Copy Condition_2 sample count summary files to Condition_2 folder M_Num_Cond2_List: 12345 ------------------------------------------ ========================================================== Number of replicates in each condition: NUM_REP_CONDITION1: 2 NUM_REP_CONDITION1: 2 ========================================================== Renaming input count files number of mapped reads (feature count summary) Status Ezh12F_1_sorted.bam Assigned 2788075 Unassigned_Ambiguity 332727 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11106743 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_2_sorted.bam Assigned 2970063 Unassigned_Ambiguity 377029 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12644126 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_3_sorted.bam Assigned 2148503 Unassigned_Ambiguity 483639 Unassigned_MultiMapping 0 Unassigned_NoFeatures 12208211 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_4_sorted.bam Assigned 2021184 Unassigned_Ambiguity 406076 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13008798 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12F_5_sorted.bam Assigned 2217112 Unassigned_Ambiguity 391910 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11640969 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12M_1_sorted.bam Assigned 2106057 Unassigned_Ambiguity 431413 Unassigned_MultiMapping 0 Unassigned_NoFeatures 13291059 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 Status Ezh12M_2_sorted.bam Assigned 1831983 Unassigned_Ambiguity 451834 Unassigned_MultiMapping 0 Unassigned_NoFeatures 11889391 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_FragmentLength 0 Unassigned_Chimera 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_Duplicate 0 ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 350676 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P140.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P140.summary -rw-r--r-- 1 kkarri waxmanlab 350162 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P141.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P141.summary -rw-r--r-- 1 kkarri waxmanlab 347859 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P142.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P142.summary -rw-r--r-- 1 kkarri waxmanlab 347539 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P143.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P143.summary -rw-r--r-- 1 kkarri waxmanlab 348553 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P144.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P144.summary -rw-r--r-- 1 kkarri waxmanlab 347218 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P140.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P140.summary -rw-r--r-- 1 kkarri waxmanlab 346617 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P141.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P141.summary -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 17 10:27 /scratch/3911212.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3911212.1.linga/Input/Ezh12F_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:27 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:27 .. /scratch/3911212.1.linga/Input/Ezh12M_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:27 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:27 .. ========================================================== Starting to run my commands Printing Rscript command: Rscript differentialAnalysis.R Ezh12M_P14 Ezh12F_P14 2 5 /unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt /scratch/3911212.1.linga/Input DiffExp_v2_LncRNA_Intronic_Only intronic_only_gene_models_ncRNA_for_counting_lengths.txt [1] "Arguments for differentialAnalysisDESeq.R:" [1] "Ezh12M_P14" [1] "Ezh12F_P14" [1] 2 [1] 5 [1] "/unprotected/projects/waxmanlab/routines/GTF_Files/ncRNA_output_filtered_final_gene.txt" [1] "/scratch/3911212.1.linga/Input" [1] "DiffExp_v2_LncRNA_Intronic_Only" [1] "intronic_only_gene_models_ncRNA_for_counting_lengths.txt" [1] "sum1:18731.5578492683" "sum1:41033.3536925232" "sum1:29882.4557708957" [1] "sum2:30538.0250195355" "sum2:34636.1638009951" "sum2:42388.3381932044" [4] "sum2:43353.7642927869" "sum2:36153.5812582354" "sum2:37413.9745129514" [1] 15558 23 [1] 15558 67 [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" "chr9" [1] "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17" "chr18" [10] "chr19" [1] "chrX" "chrY" [1] "output file is in: /scratch/3911212.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_Ezh12M_P14_Ezh12F_P14.txt" ========================================================== Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver3.R DiffExp_v2_LncRNA_Intronic_Only_Ezh12M_P14_Ezh12F_P14.txt Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only Create SEGEX formatted file: Printing Rscript command: Rscript formatForSegex_ver4.R DiffExp_v2_LncRNA_Intronic_Only_Ezh12M_P14_Ezh12F_P14.txt Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload 1 LncRNA_Intronic_Only ========================================================== Comparison_Info: Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12 #---------------------------------------------------------------------------------- Running Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: Rscript Diff_Genes.R Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt 2 0.05 DESeq LncRNA_Intronic_Only'_'Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "DESeq" [1] "count_method:" [1] "LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 0 7 [1] "Check out Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt!" [1] "Check out Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt!" Rscript Diff_Genes.R Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt 2 0.05 EdgeR LncRNA_Intronic_Only'_'Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12 [1] "Print arguments:" [1] "-----------------" [1] "Differential expression_Output:" [1] "Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt" [1] "fold_change_cutoff:" [1] "2" [1] "padj_cutoff:" [1] "0.05" [1] "postfix:" [1] "EdgeR" [1] "count_method:" [1] "LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12" [1] "-----------------" [1] "Differential Gene Counts" [1] "Number of significant differential genes with positive fold change (Up Genes):" [1] 0 7 [1] "Number of significant differential genes with negative fold change (Down Genes):" [1] 1 7 [1] "Check out Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt!" [1] "Check out Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt!" #---------------------------------------------------------------------------------- Running Venn_Diff_Genes.R #---------------------------------------------------------------------------------- Printing Rscript command: #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt LncRNA_Intronic_Only_Counting DiffExp_15g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt" [1] "File2:" [1] "Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_15g" [1] "-----------------" [1] "Down.DESeq.Intronic_Only.HTSeq" [1] "Down.EdgeR.Intronic_Only.HTSeq" null device 1 [1] "Removing VennDiagram*.log files" [1] "Check out Venn diagram and Count.Table!" #---------------------------------------------------------------------------------- Rscript Venn_Diff_Genes.R Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt LncRNA_Intronic_Only_Counting DiffExp_15g [1] "Print arguments:" [1] "-----------------" [1] "File1:" [1] "Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt" [1] "File2:" [1] "Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt" [1] "Subtitle:" [1] "LncRNA_Intronic_Only_Counting" [1] "DiffExp_Index:" [1] "DiffExp_15g" [1] "-----------------" [1] "Up.DESeq.Intronic_Only.HTSeq" [1] "Up.EdgeR.Intronic_Only.HTSeq" #---------------------------------------------------------------------------------- #---------------------------------------------------------------------------------- Merging Count.Table(s) into one text file #---------------------------------------------------------------------------------- Comparison_Info: Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12 #---------------------------------------------------------------------------------- ========================================================== Renaming the Differential_Expression_File ========================================================== List files in Input -rw-r--r-- 1 kkarri waxmanlab 167 Mar 17 10:28 /scratch/3911212.1.linga/Input/DiffExp_15g_Venn_Tables_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 4349081 Mar 17 10:28 /scratch/3911212.1.linga/Input/DiffExp_v2_LncRNA_Intronic_Only_Ezh12M_P14_Ezh12F_P14.txt -rwxr-xr-x 1 kkarri waxmanlab 7706 Mar 17 10:27 /scratch/3911212.1.linga/Input/Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 229 Mar 17 10:28 /scratch/3911212.1.linga/Input/Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 290 Mar 17 10:28 /scratch/3911212.1.linga/Input/Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 350676 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P140.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P140.summary -rw-r--r-- 1 kkarri waxmanlab 350162 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P141.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P141.summary -rw-r--r-- 1 kkarri waxmanlab 347859 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P142.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P142.summary -rw-r--r-- 1 kkarri waxmanlab 347539 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P143.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P143.summary -rw-r--r-- 1 kkarri waxmanlab 348553 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P144.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12F_P144.summary -rw-r--r-- 1 kkarri waxmanlab 1545786 Mar 17 10:28 /scratch/3911212.1.linga/Input/Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 1623576 Mar 17 10:28 /scratch/3911212.1.linga/Input/Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 650731 Mar 17 10:28 /scratch/3911212.1.linga/Input/Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq.txt -rw-r--r-- 1 kkarri waxmanlab 823829 Mar 17 10:28 /scratch/3911212.1.linga/Input/Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR.txt -rw-r--r-- 1 kkarri waxmanlab 347218 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P140.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P140.summary -rw-r--r-- 1 kkarri waxmanlab 346617 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P141.out -rw-r--r-- 1 kkarri waxmanlab 299 Mar 17 10:27 /scratch/3911212.1.linga/Input/Ezh12M_P141.summary -rw-r--r-- 1 kkarri waxmanlab 229 Mar 17 10:28 /scratch/3911212.1.linga/Input/Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 229 Mar 17 10:28 /scratch/3911212.1.linga/Input/Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12.txt -rw-r--r-- 1 kkarri waxmanlab 2204 Mar 17 10:28 /scratch/3911212.1.linga/Input/VennDiagram2020-03-17_10-28-26.log -rwxr-xr-x 1 kkarri waxmanlab 9993 Mar 17 10:27 /scratch/3911212.1.linga/Input/Venn_Diff_Genes.R -rw-r--r-- 1 kkarri waxmanlab 33523 Mar 17 10:28 /scratch/3911212.1.linga/Input/Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq.png -rwxr-xr-x 1 kkarri waxmanlab 4968 Mar 17 10:27 /scratch/3911212.1.linga/Input/formatForSegex_ver3.R -rwxr-xr-x 1 kkarri waxmanlab 4972 Mar 17 10:27 /scratch/3911212.1.linga/Input/formatForSegex_ver4.R -rw-r--r-- 1 kkarri waxmanlab 414633 Mar 17 10:27 /scratch/3911212.1.linga/Input/intronic_only_gene_models_ncRNA_for_counting_lengths.txt /scratch/3911212.1.linga/Input/Ezh12F_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:27 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:28 .. /scratch/3911212.1.linga/Input/Ezh12M_P14: total 8 drwxr-xr-x 2 kkarri waxmanlab 4096 Mar 17 10:27 . drwxr-xr-x 4 kkarri waxmanlab 4096 Mar 17 10:28 .. ========================================================== List files in scratch total 3.4M drwx------ 3 kkarri waxmanlab 4.0K Mar 17 10:28 . drwxrwxrwt. 23 root root 4.0K Mar 17 10:27 .. -rw-r--r-- 1 kkarri waxmanlab 87 Mar 17 10:27 Condition_1.txt -rw-r--r-- 1 kkarri waxmanlab 168 Mar 17 10:27 Condition_2.txt drwxr-xr-x 4 kkarri waxmanlab 4.0K Mar 17 10:28 Input -rwxr-xr-x 1 kkarri waxmanlab 15K Mar 17 10:27 differentialAnalysis.R -rw-r--r-- 1 kkarri waxmanlab 3.3M Mar 17 10:27 ncRNA_output_filtered_final_gene.txt ========================================================== Re-naming files in OUTPUT_DIR Need to append the COUNT_PROGRAM name to all output files List files in OUTPUT_DIR total 21M drwxr-xr-x 2 kkarri waxmanlab 4.0K Mar 17 10:21 . drwxr-xr-x 7 kkarri waxmanlab 4.0K Mar 17 10:20 .. -rw-r--r-- 1 kkarri waxmanlab 167 Mar 17 10:21 DiffExp_15g_Venn_Tables_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 4.2M Mar 17 10:21 DiffExp_v2_LncRNA_Intronic_Only_Ezh12M_P14_Ezh12F_P14_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 229 Mar 17 10:21 Down_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 290 Mar 17 10:21 Down_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.5M Mar 17 10:21 Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 1.6M Mar 17 10:21 Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 636K Mar 17 10:21 Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_DESeq_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 805K Mar 17 10:21 Ezh12F_P14_GSE118757_12345_vs_Ezh12M_P14_GSE118757_12_DiffExp_v2_LncRNA_Intronic_Only_forSEGEXUpload_TPM_EdgeR_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 229 Mar 17 10:21 Up_Genes_DESeq_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 229 Mar 17 10:21 Up_Genes_EdgeR_LncRNA_Intronic_Only_Ezh12F_P14_GSE118757_12345_Ezh12M_P14_GSE118757_12_featureCounts.txt -rw-r--r-- 1 kkarri waxmanlab 33K Mar 17 10:21 Venn_Down.DESeq.Intronic_Only.HTSeq.Down.EdgeR.Intronic_Only.HTSeq_featureCounts.png ========================================================== ========================================================== Finished on : Tue Mar 17 10:28:28 EDT 2020 0 minutes and 54 seconds elapsed. ==========================================================